How to link RNA families to pdb ids (RNA family label)

[OliviaViessmann]

Hello,
I am trying to match the pdb_chain_id to RNA family labels. Is there a dictionary/json with the mapping?
I wasn't able to find it browsing through the repo.

Thank you in advance
Olivia

[marcellszi]

Hi @OliviaViessmann,

There is no dictionary/JSON that directly maps the families to the chains. See #5 for a discussion on the topic.

We have the output of the Infernal search 2024-04-26-full-cmscan.tbl which contains this information. The Tabular API can be used to read these files a lot like a dictionary. See this example.

If you really wanted this information in a Python dictionary, it is very easy to do this with the Tabular API. You could do something like:

from rna3db.tabular import read_tbls_from_dir
from collections import defaultdict
tbl = read_tbls_from_dir('data/') #NOTE: this is the *directory* containing the .tbl file(s)
family_dict = defaultdict(list)
for hit in tbl:
    family_dict[hit.query_name].append(hit._asdict())

This will create a dictionary that maps the name of the chains to a list of the hits for that chain. Each hit is a dictionary that contains the usual keys (target_name, target_accession, etc.).